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- PDB-2k6t: Solution structure of the relaxin-like factor -

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Basic information

Entry
Database: PDB / ID: 2k6t
TitleSolution structure of the relaxin-like factor
Components
  • Insulin-like 3 A chain
  • Insulin-like 3 B chain
KeywordsHORMONE / protein / Cleavage on pair of basic residues / Disease mutation / Polymorphism / Secreted
Function / homology
Function and homology information


Relaxin receptors / positive regulation of wound healing / positive regulation of epithelial cell migration / insulin receptor binding / hormone activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell-cell signaling / protease binding / spermatogenesis / G alpha (s) signalling events ...Relaxin receptors / positive regulation of wound healing / positive regulation of epithelial cell migration / insulin receptor binding / hormone activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell-cell signaling / protease binding / spermatogenesis / G alpha (s) signalling events / signaling receptor binding / extracellular space / extracellular region
Similarity search - Function
Insulin-like INSL3/INSL4 / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsBullesbach, E.E. / Hass, M.A.S. / Jensen, M.R. / Hansen, D.F. / Kristensen, S.M. / Schwabe, C. / Led, J.J.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structure of a conformationally restricted fully active derivative of the human relaxin-like factor
Authors: Bullesbach, E.E. / Hass, M.A.S. / Jensen, M.R. / Hansen, D.F. / Kristensen, S.M. / Schwabe, C. / Led, J.J.
History
DepositionJul 23, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-like 3 A chain
B: Insulin-like 3 B chain


Theoretical massNumber of molelcules
Total (without water)6,3062
Polymers6,3062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Insulin-like 3 A chain / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor / RLF


Mass: 2778.189 Da / Num. of mol.: 1 / Fragment: UNP residues 106-131 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P51460
#2: Protein/peptide Insulin-like 3 B chain / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor / RLF


Mass: 3528.118 Da / Num. of mol.: 1 / Fragment: UNP residues 25-55 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P51460
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
8122D DQF-COSY
9222D DQF-COSY
6312D DQF-COSY
9422D 1H-1H TOCSY
6512D 1H-1H TOCSY
9622D 1H-13C HSQC
8722D 1H-1H NOESY
9822D 1H-1H NOESY
1912D 1H-1H NOESY
21012D 1H-1H NOESY
31112D 1H-1H NOESY
41212D 1H-1H NOESY
51312D 1H-1H NOESY
61412D 1H-1H NOESY
71512D 1H-1H NOESY
61612D 1H-15N HSQC
91722D 1H-13C HSQC
51832D 1H-15N HSQC
51932D 1H-15N HSQC-NOESY
NMR detailsText: structure was determined using homonuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 mM RLF; H2O sodium acetate, 0.2 mM RLF; H2O sodium acetate, 0.3 mM RLF; H2O sodium acetate, 0.6 mM RLF; H2O sodium acetate, 1.2 mM RLF; H2O sodium acetate, 92% H2O/8% D2O92% H2O/8% D2O
21.2 mM RLF; D2O sodium acetate, 1.2 mM RLF; D2O, 100% D2O100% D2O
31.2 mM [U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119) RLF; H2O sodium acetate, 0.6 mM [U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119) RLF; H2O sodium acetate, 0.4 mM [U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119) RLF; H2O sodium acetate, 0.2 mM [U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119) RLF; H2O sodium acetate, 92% H2O/8% D2O92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMRLF; H2O sodium acetate1
0.2 mMRLF; H2O sodium acetate2
0.3 mMRLF; H2O sodium acetate3
0.6 mMRLF; H2O sodium acetate4
1.2 mMRLF; H2O sodium acetate5
1.2 mMRLF; D2O sodium acetate6
1.2 mMRLF; D2O7
1.2 mMRLF; H2O sodium acetate[U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119)8
0.6 mMRLF; H2O sodium acetate[U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119)9
0.4 mMRLF; H2O sodium acetate[U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119)10
0.2 mMRLF; H2O sodium acetate[U-15N] Gly(47), Gly(48), Ala(107), Ala(112), Gly(119)11
Sample conditions
Conditions-IDpHTemperature (K)
15293 K
25296 K
35301 K
45303 K
55306 K
65308 K
75313 K
8288 K
9308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
ARIA2.1Linge, O'Donoghue and Nilgesnoe assignment
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
Sparky3.11Goddardpeak picking
Sparky3.11Goddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PREDITORWishartbond angle prediction
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1154 / NOE intraresidue total count: 506 / NOE long range total count: 182 / NOE medium range total count: 208 / NOE sequential total count: 258
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 6 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.053 Å / Distance rms dev error: 0.0015 Å

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